Alignments for a candidate for ilvD in Saccharomonospora cyanea NA-134

GapMind for Amino acid biosynthesis

Alignments for a candidate for ilvD in Saccharomonospora cyanea NA-134

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate WP_005456798.1 SACCYDRAFT_RS13145 dihydroxy-acid dehydratase

Query= SwissProt::P9WKJ5
         (575 letters)



>NCBI__GCF_000244975.1:WP_005456798.1
          Length = 560

 Score =  667 bits (1722), Expect = 0.0
 Identities = 339/560 (60%), Positives = 412/560 (73%), Gaps = 5/560 (0%)

Query: 16  DIKPRSRDVTDGLEKAAARGMLRAVGMDDEDFAKPQIGVASSWNEITPCNLSLDRLANAV 75
           D + RSR VTDG+ +A AR MLRAVG  DEDF +PQIGVA++ N++TPCN++LDRLA A 
Sbjct: 2   DPRHRSRIVTDGVTRAPARAMLRAVGFADEDFTRPQIGVAAAANDLTPCNIALDRLAGAT 61

Query: 76  KEGVFSAGGYPLEFGTISVSDGISMGHEGMHFSLVSREVIADSVEVVMQAERLDGSVLLA 135
            +GV  AGG  + F TI++SDGI+MGH GM  SL SR++IADSVE VM+AE+LD  V +A
Sbjct: 62  ADGVRKAGGVAMRFSTIAMSDGIAMGHRGMRASLPSRDLIADSVECVMEAEQLDAMVTIA 121

Query: 136 GCDKSLPGMLMAAARLDLAAVFLYAGSILPGRAKLSDGSERDVTIIDAFEAVGACSRGLM 195
           GCDKSLPGMLMAAARL++   FLY GS LPG         R VTI D FEAVGA + GL+
Sbjct: 122 GCDKSLPGMLMAAARLNVPTAFLYGGSSLPG-----SWQGRPVTIQDVFEAVGAQASGLL 176

Query: 196 SRADVDAIERAICPGEGACGGMYTANTMASAAEALGMSLPGSAAPPATDRRRDGFARRSG 255
           S  D+D +ERA CPG G+C GMYTANT+A+ AEALG++LPGSA+ PA D  R G A  +G
Sbjct: 177 STDDLDELERAACPGAGSCAGMYTANTIAAEAEALGIALPGSASAPAIDPTRPGIAHDTG 236

Query: 256 QAVVELLRRGITARDILTKEAFENAIAVVMAFGGSTNAVLHLLAIAHEANVALSLQDFSR 315
            A V  LR GI  RDILT+EAFENAI VVMA GGSTNA LHL AIAHEA V L+L DF R
Sbjct: 237 AAAVAALRAGIRPRDILTREAFENAITVVMALGGSTNAALHLPAIAHEAGVRLTLDDFDR 296

Query: 316 IGSGVPHLADVKPFGRHVMSDVDHIGGVPVVMKALLDAGLLHGDCLTVTGHTMAENLAAI 375
           I    PH+AD++P GRHVM+D+  +GGVP V+ ALLDAGLLHGDCLTVTG T+AENLA +
Sbjct: 297 ISRHTPHIADLRPGGRHVMADLHQVGGVPAVLAALLDAGLLHGDCLTVTGATLAENLAEL 356

Query: 376 TPPDPDGKVLRALANPIHPSGGITILHGSLAPEGAVVKTAGFDSDVFEGTARVFDGERAA 435
             P PDG VLR   +P+ P GG+ IL G+LAP GAVVK AG   D F GTARVFD E AA
Sbjct: 357 AAPKPDGTVLRTPDDPLRPDGGLAILRGALAPSGAVVKMAGLTVDRFHGTARVFDNEDAA 416

Query: 436 LDALEDGTITVGDAVVIRYEGPKGGPGMREMLAITGAIKGAGLGKDVLLLTDGRFSGGTT 495
           +  +  G +T G+ +VIRYEGP+GGPGM EMLA+T A++G GLG  V L+TDGRFSG TT
Sbjct: 417 MGYVSGGRLTAGEVIVIRYEGPRGGPGMPEMLAVTAAVRGTGLGDQVALVTDGRFSGATT 476

Query: 496 GLCVGHIAPEAVDGGPIALLRNGDRIRLDVAGRVLDVLADPAEFASRQQDFSPPPPRYTT 555
           GLCVGH+APEA  GGP+AL+ +GD I +D+  R +D+  +PAE   R+  + PPP     
Sbjct: 477 GLCVGHVAPEAAAGGPLALVADGDPIMIDIPARTIDLDVNPAELERRRHRWHPPPAPTGN 536

Query: 556 GVLSKYVKLVSSAAVGAVCG 575
           G L+KY +LV  A+ GA+ G
Sbjct: 537 GFLAKYSRLVGCASQGALVG 556


Lambda     K      H
   0.318    0.136    0.393 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1117
Number of extensions: 46
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 575
Length of database: 560
Length adjustment: 36
Effective length of query: 539
Effective length of database: 524
Effective search space:   282436
Effective search space used:   282436
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate WP_005456798.1 SACCYDRAFT_RS13145 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR00110.hmm
# target sequence database:        /tmp/gapView.12649.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR00110  [M=543]
Accession:   TIGR00110
Description: ilvD: dihydroxy-acid dehydratase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                 Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-220  719.1   1.0     2e-220  718.9   1.0    1.0  1  lcl|NCBI__GCF_000244975.1:WP_005456798.1  SACCYDRAFT_RS13145 dihydroxy-aci


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000244975.1:WP_005456798.1  SACCYDRAFT_RS13145 dihydroxy-acid dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  718.9   1.0    2e-220    2e-220       1     540 [.      18     554 ..      18     557 .. 0.99

  Alignments for each domain:
  == domain 1  score: 718.9 bits;  conditional E-value: 2e-220
                                 TIGR00110   1 aarallkatGlkdedlekPiiavvnsyteivPghvhlkdlaklvkeeieaaGgvakefntiavsDGiam 69 
                                               +ara+l+a+G+ ded+++P+i+v+ + ++++P+++ l+ la + ++++++aGgva++f tia+sDGiam
  lcl|NCBI__GCF_000244975.1:WP_005456798.1  18 PARAMLRAVGFADEDFTRPQIGVAAAANDLTPCNIALDRLAGATADGVRKAGGVAMRFSTIAMSDGIAM 86 
                                               579****************************************************************** PP

                                 TIGR00110  70 gheGmkysLpsreiiaDsvetvvkahalDalvvissCDkivPGmlmaalrlniPaivvsGGpmeagktk 138
                                               gh+Gm+ sLpsr++iaDsve v++a++lDa+v+i+ CDk +PGmlmaa+rln+P+ + +GG+  +g  +
  lcl|NCBI__GCF_000244975.1:WP_005456798.1  87 GHRGMRASLPSRDLIADSVECVMEAEQLDAMVTIAGCDKSLPGMLMAAARLNVPTAFLYGGSSLPGSWQ 155
                                               ********************************************************************* PP

                                 TIGR00110 139 lsekidlvdvfeavgeyaagklseeeleeiersacPtagsCsGlftansmacltealGlslPgsstlla 207
                                                ++ +++ dvfeavg+ a+g ls ++l+e+er acP+agsC+G++tan++a+ +ealG++lPgs++++a
  lcl|NCBI__GCF_000244975.1:WP_005456798.1 156 -GRPVTIQDVFEAVGAQASGLLSTDDLDELERAACPGAGSCAGMYTANTIAAEAEALGIALPGSASAPA 223
                                               .9******************************************************************* PP

                                 TIGR00110 208 tsaekkelakksgkrivelvkknikPrdiltkeafenaitldlalGGstntvLhllaiakeagvklsld 276
                                               ++  +  +a+ +g+  v +++  i+Prdilt+eafenait+++alGGstn+ Lhl+aia+eagv+l+ld
  lcl|NCBI__GCF_000244975.1:WP_005456798.1 224 IDPTRPGIAHDTGAAAVAALRAGIRPRDILTREAFENAITVVMALGGSTNAALHLPAIAHEAGVRLTLD 292
                                               ********************************************************************* PP

                                 TIGR00110 277 dfdrlsrkvPllaklkPsgkkviedlhraGGvsavlkeldkegllhkdaltvtGktlaetlekvkvlrv 345
                                               dfdr+sr++P++a+l+P+g++v++dlh++GGv+avl  l  +gllh d+ltvtG tlae+l++    + 
  lcl|NCBI__GCF_000244975.1:WP_005456798.1 293 DFDRISRHTPHIADLRPGGRHVMADLHQVGGVPAVLAALLDAGLLHGDCLTVTGATLAENLAELAAPKP 361
                                               *******************************************************************99 PP

                                 TIGR00110 346 dqdvirsldnpvkkegglavLkGnlaeeGavvkiagveedilkfeGpakvfeseeealeailggkvkeG 414
                                               d  v+r+ d+p++ +ggla+L+G la+ Gavvk+ag      +f+G+a+vf++e++a+  + gg++++G
  lcl|NCBI__GCF_000244975.1:WP_005456798.1 362 DGTVLRTPDDPLRPDGGLAILRGALAPSGAVVKMAGLTV--DRFHGTARVFDNEDAAMGYVSGGRLTAG 428
                                               ************************************986..89************************** PP

                                 TIGR00110 415 dvvviryeGPkGgPGmremLaPtsalvglGLgkkvaLitDGrfsGgtrGlsiGhvsPeaaegGaialve 483
                                               +v+viryeGP+GgPGm+emLa t+a+ g GLg++vaL+tDGrfsG+t+Gl++Ghv+Peaa+gG++alv 
  lcl|NCBI__GCF_000244975.1:WP_005456798.1 429 EVIVIRYEGPRGGPGMPEMLAVTAAVRGTGLGDQVALVTDGRFSGATTGLCVGHVAPEAAAGGPLALVA 497
                                               ********************************************************************* PP

                                 TIGR00110 484 dGDkikiDienrkldlevseeelaerrakakkkearevkgaLakyaklvssadkGav 540
                                               dGD i+iDi++r++dl+v+ +el++rr++++++ a + +g+Laky++lv  a++Ga+
  lcl|NCBI__GCF_000244975.1:WP_005456798.1 498 DGDPIMIDIPARTIDLDVNPAELERRRHRWHPPPAPTGNGFLAKYSRLVGCASQGAL 554
                                               *******************************************************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (543 nodes)
Target sequences:                          1  (560 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 10.43
//
[ok]

This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis